Integrated protein affinity capture centrifugation device

ABSTRACT

A method and apparatus are described for screening a proteome comprising an array of affinity elements, whereby a proteome is directed through the affinity array and those components that specifically bind to the affinity array are eluted in a suitable eluent by means of centrifugation. Suitable eluents can include a proteome component, a chemical library component or an affinity element. This method and apparatus can be used for several purposes, including screening for bio-active compounds, determining physiological targets of known drugs, determining specificity of compound interactions with physiological targets, and for quantitative protein analyses.

BACKGROUND OF THE INVENTION

[0001] Proteomics is an emerging technology for the study of proteinfunction that has arisen in the post-genomics era. As the entire genomesof different organisms of the animal, plant, prokaryotic and viralkingdoms are being sequenced, thousands of genes are being identified,and these genes encode an abundance of distinct proteins. Theseproteins, the proteome of an organism, are being studied foridentification of new drugs or commercially-important bio-activemolecules.

[0002] Now the search for better therapeutics is being driven by severalfactors which need to be discovered: the identity and role of proteintargets whose function may be pivotal for disease progression; themolecules that interact with these protein targets to attenuate theirfunction and cause a therapeutic effect; the key biochemical pathwaysand the manner in which proteins interact with each other, which iscritical for the selection of the most appropriate target fortherapeutic intervention; and the impact of therapeutic candidates onthe whole organism, including the most common variants of importantproteins to identify potential side-effects and toxicity (thepharmacogenomic profile) of drug candidates as rapidly as possible.

[0003] The traditional approaches to drug discovery are either byselective drug design methods, which to date are at best, an inexactscience, or by screening test compounds in a disease model. Screening,historically, has been the most effective of the two methods foridentifying therapeutics, but it is labor-intensive. Most screening hasbeen of randomly-selected candidates. More recently, screening hasincluded the use of combinatorial libraries of candidate drugs, orportion thereof. Generally however, the techniques used to screenlibraries, such as liquid chromatography, have been slow and expensive.

[0004] Therefore, a need exists for an apparatus and method to screencandidate therapeutic drugs that significantly reduce of eliminate theabove-mentioned problems.

SUMMARY OF THE INVENTION

[0005] The present invention is generally directed to a method forscreening a proteome, which is a mixture of proteins or compoundsderived from a common source, and an apparatus for screening a proteome.

[0006] In one embodiment, the method for screening a proteome includespassing the proteome though an array of elements that possess anaffinity for at least one compound in the proteome. This is followed bywashing the array to remove those compounds of the proteome that do notspecifically bind, and subsequently directing an eluent through thearray by centrifugal force, which releases the specifically-boundcompound, and elutes the released compound, thereby screening theproteome.

[0007] In another embodiment, an apparatus is provided to screen aproteome. The apparatus includes an array of affinity elements thatincludes at least one ligand, and means to apply a centrifugal force tothe array such that, in the presence of an eluent, the compound of theproteome that is bound to the ligand can be eluted from the affinityelement by centrifugation.

[0008] This invention has many advantages. For example, proteomes can bescreened rapidly and systematically, whereby not only new lead compoundscan be identified, but also the identity of the physiological targets ofknown drugs. Use of an affinity array enables efficient and quantitativecapture of proteins, even when proteins are present in small quantities.This is important since disease-causing proteins, such as transcriptionfactors or kinases, are often present in low copy numbers in a cell.Furthermore, the amount of protein captured can be directly measured.The use of small bed volumes of resin enables the enrichment of targetedproteins and proteomes. By employing centrifugal force to direct aneluent through the affinity array, the total volume of the eluentapplied to the array can be recovered, which contrasts with flow-typeelution methods that generally result in larger elution volumes andtherefore greater dilution of the eluate. Thus, relatively small volumesof eluents can be applied to the affinity array, which can result insignificantly more efficient recovery of proteins that are readilyamenable to subsequent manipulation. For example, because the elutedproteins are concentrated in a small volume, they typically can bedirectly sampled for MALDI-TOF mass spectrometry or ICAT analysiswithout further manipulation. This generally provides for more rapididentification of targets. Furthermore, potential toxicity can beassessed by sequencing proteins that are simultaneously eluted. Unlikemany known methods of designing improved therapeutic compounds, thisinvention can also be used to identify physiological targets of knowndrugs, the mechanism of action of which was previously unknown. Byidentifying the physiological target of the known drug using thisinvention, the mechanism of action can be assessed and improved targetscan be identified. Furthermore, this invention can be automated andintegrated into a robotics system.

BRIEF DESCRIPTION OF THE DRAWINGS

[0009]FIG. 1 is a schematic representation of a stacked columncentrifugal liquid chromatography apparatus suitable for conducting themethod of the invention.

[0010]FIG. 2 depicts a sheet of affinity column discs and the stackingof tubes of sample on top of a sheet of affinity column discs on top ofcollection tubes in 96 well-type format.

[0011]FIG. 3 depicts collection trays which can be controlled in an openor closed position according to the position of the valves.

[0012]FIG. 4 represents a single column with a sliding tell disc.

[0013]FIG. 5 is a schematic representation of a stacked columncentrifugal liquid chromatography apparatus suitable for conducting themethod of the invention which can be remotely controlled.

[0014]FIG. 6 details a general method to sequentially apply eluents andcollect eluates through a stacked column centrifugal liquidchromatography apparatus.

[0015]FIG. 7 is a schematic representation of an apparatus suitable forconducting the method of the invention that uses an array ofnano-needles to collect eluates for analysis.

[0016]FIG. 8 depicts a nano-needle array apparatus placed into a massspectrometer apparatus suitable for practicing the method of theinvention.

[0017]FIG. 9 is a detailed schematic representation of a nano-needleapparatus aligned with a mass spectrometer inlet orifice, which would besuitable for conducting the method of the invention.

DETAILED DESCRIPTION OF THE INVENTION

[0018] The features and other details of this invention, either as stepsof the invention or as combinations of parts of the intention, will nowbe more particularly described and pointed out in the claims. It will beunderstood that the particular embodiments of the invention are shown byway of illustration and not as limitations of the invention. Theprinciple features of this invention can be employed in variousembodiments without departing form the scope of the invention.

[0019] Affinity element as defined herein, refers to a component that isa candidate for interacting with, or being a ligand for, at least oneelement in a proteome or combinatorial library. Such affinity elementsinclude, but are not limited to, purines and purine analogs such as ATP,AMP, ADP, NADH. Also included are chemical, peptide or oligonucleotidelibraries, which may be separately screened with a proteome or portionthereof.

[0020] The present invention is generally directed to a method andapparatus for screening a proteome for bio-active compounds of interest.Typical methods already known in the art for screening a proteome aredescribed in WO 00/636694, filed Apr. 12, 2000, the teachings of whichare incorporated herein by reference in its entirety.

[0021] Referring to FIG. 1, shown therein is apparatus 10, which is oneembodiment of apparatus that is suitable for practicing the method ofthe invention. The apparatus includes a centrifuge, which can betemperature-regulated, with rotor 12, attached to spindle 14, to whichrotor arms 16 are attached. To rotor arms 16, one or more fluid conduits18 and 20 are connected, which supplies fluid from fluid sources 22 and24, respectively. The fluids from fluid sources 22 and 24 can beregulated by valve 26. Attached to the end of rotor arms 16 is hinge 28,to which stacked trays 30 are attached. The application of a centrifugalforce about the axis of rotation will cause stacked trays 30 to rotateabout hinge 28 and thereby cause stacked trays 30 to become parallelwith the centrifugal force. In one embodiment, stacked trays 30 includesample tray 32, also referred to herein as a tube sheet, that containsample, for example and without limitation, a proteome sample orfraction thereof, or a combinatorial library sample or fraction thereof.In a further embodiment, the stacked trays include at least one traythat contains affinity array 34 to be screened, and at least one tray 36that can collect eluate.

[0022] To perform the screening of affinity array 34, a centrifugalforce is applied to stacked trays 30. Compounds specifically bound toaffinity array 34 are eluted from affinity array 34 by means ofdirecting at least one eluent through affinity array 34 bycentrifugation, wherein the eluent releases the bound compounds fromaffinity array 34 as a component of the eluate, thereby screening theproteome. In one embodiment, sample in array 32 depicted in FIG. 1,flows through affinity array 34. Compounds of the sample in array 32that specifically bind to an affinity element of affinity array 34 areretained in affinity array 34, whereas compounds that do not bind to theaffinity element elute into collection array 36. Additionally oralternatively, the means of applying an eluent to an array can bethrough one or more conduits 18 or 20 that can be further regulated atvalve 26. In a further embodiment, at least affinity array 34 can bewashed before and/or after applying the sample, by applying a washsolution to affinity array 34 using centrifugation, thereby removingnon-specifically binding components from affinity array 34. In oneembodiment, the wash solution is a low ionic buffer. In anotherembodiment, the wash solution is a high ionic buffer. Thespecifically-bound compounds are eluted from affinity array 34 by meansof directing at least one eluent through affinity array 34 bycentrifugation, wherein the eluent releases the bound compounds from theaffinity element as a component of the eluate. Waste materials can beremoved from the centrifuge unit by means of waste conduit 38.

[0023] In one embodiment, stacked trays 30 are contained within a swingbasket or bucket that can support stacked trays 30.

[0024] As represented in FIG. 2, affinity array 34 includes suitableaffinity elements 35. Examples of suitable affinity elements 35 arecolumns or discs. In one embodiment, affinity array 34 includes at leasttwelve affinity elements. In another embodiment, affinity array 34includes at least ninety-six affinity elements. Affinity array 34 can belocated between arrays 32 and 36 so that one or more affinity elementscan be aligned with the affinity elements of affinity array 34, or theaffinity elements can be intentionally misaligned. In one embodiment,affinity array 34 has at least one element that is at least onephysiological target candidate or ligand of a protein component of theproteome to be screened. In a preferred embodiment, the physiologicaltarget is adenosine triphosphate (ATP) or a structural analog thereof.In a specific embodiment, the ATP is bound to an inert support in auniform orientation. Inert supports suitable for use in the inventionwill be recognized by those of skill in the art. Without limitation,examples of suitable resins for use as an inert support include bead ormonolithic resins, such as those used for chromatography, and which arecomposed of a base matrix such as polyacrylamide, agarose, coatedsilica-beads, cellulose, polystyrene divinylbenzene, methacrylate orpolymethacrylate, and the like. Typically, a suitable polyacrylamideinert support can be selected from CM Hyper D® (F grade) and ceramicHyper D®; a suitable agarose inert support can be Sepharose® Fast Flow;a suitable silica inert support can be BAKERBOND PEI™; a suitablepolystyrene divinylbenzene inert support can be Amberchrom®; a suitablemethacrylate or polymethacrylate inert support can be selected fromMacro-Prep® DEAE, and Macro-Prep® high S, a suitable hydrophilic polymermatrix inert support can be Toyopearl® Butyl-650M; and a suitablecomposite or monlithic inert support can be selected from UNO Sphere Qand UNO™Sphere S. Preferably, the ATP is bound to the inert support atthe gamma phosphate portion of the ATP, thus exposing the adenosineportion of the ATP to solutions or eluents directed through the array.Typical methods already known in the art for linking an ATP moiety to aninert support are described in U.S. Pat. No. 5,536,822, filed Mar. 9,1994, the teachings of which are incorporated herein by reference intheir entirety. In another preferred embodiment, the eluent comprises atleast one purine or purine analog. In one embodiment, the purine analogis naturally-occurring. In a specific embodiment, the purine analog isselected from the group consisting of NADH, AMP, ADP and ATP.

[0025] In another embodiment, the physiological target is bound to aninert support in an orientation different from an identicalphysiological target bound to another inert support in anotherorientation.

[0026] Another embodiment of the invention provides for each element inaffinity array 34 to have a plurality of physiological targets orligands. In a particularly preferred embodiment, the number ofphysiological targets or ligands in each element in affinity array 34 isat least about ten. A further embodiment of this invention provides forthe whole proteome of interest to be distributed among the elements ofaffinity array 34.

[0027] In a further embodiment of the invention, the concentration ofthe physiological target on at least a portion of the elements ofaffinity array 34 is at least about 50 μmoles to at least about 100μmoles per milliliter of element. More preferably the concentration ofthe physiological target on at least a portion of the elements ofaffinity array 34 is at least about 10 μmoles per milliliter of theelement.

[0028] Furthermore, in another preferred embodiment, the amount ofproteome that is directed through affinity array 34 is sufficient torecover at least about 0.1 pmol to at least about 1 pmol of a componentof the proteome that binds to the physiological target on affinity array34.

[0029] Generally, the eluent includes a component from a chemicallibrary in a concentration ranging from about 1 nM to about 500 mM, morepreferably ranging from about 10 nM to about 1 mM. The chemical librarycomponent of the eluent includes at least a single molecule. In apreferred embodiment, the chemical library component includes at leastten structurally non-related molecules. The component of the chemicallibrary is preferably soluble in a physiologically-compatible solution.In a preferred embodiment the physiologically-compatible solution is anaqueous solution. In an alternative embodiment, the solution contains anorganic solvent. An example of an organic solvent solution is dimethylsulphoxide (DMSO), preferably in a concentration range of up to about10% (volume/volume).

[0030] In an additional embodiment, the elements of affinity array 34and the eluent each include a portion of at least one chemical library.

[0031] In another embodiment of the invention, at least a portion of theelements of affinity array 34 includes an amount of resin packing in arange of between about 50 μl and about 100 μl.

[0032] Preferably, the volume of eluent directed through each affinityelement 35 of array 34 is in a range of between about 10 μl and about100 μl. In one embodiment, the eluent includes a single component whichis a candidate for selective release of a proteome component fromaffinity element 35. In a further embodiment, the eluent includes aplurality of distinct components that are candidates for the ability toselectively release and elute a proteome component from affinity element35. Additionally, one embodiment of the invention provides for theeluent to include at least about ten distinct components that arecandidates for release of a proteome component from affinity element 35.In another embodiment, the eluent includes at least a portion of achemical library.

[0033] In one embodiment, affinity array 34 is screened by competitivebinding with an eluent containing a proteome component. In anotherembodiment, affinity array 34 is screened by competitive binding with aneluent containing an affinity element. In an alternative embodiment,affinity array 34 is screened by competitive binding with an eluentcontaining a chemical library component.

[0034] It is believed that use of these arrays provide flexibility inthe types of combinations of proteins, substrates and targets in acombinatorial library that can be effectively screened. Together withthe control over experimental conditions possible with centrifugation, awide variety of targets can be screened in a small fraction of the timegenerally necessary using known techniques.

[0035] In one embodiment of the apparatus of the invention, as depictedin FIG. 3, stacked trays of tube sheets or collection trays 36 can beseparated by means of slider valves 42, which can be positioned suchthat the open position of the valve is aligned with the orifices of twoadjacent tube sheets or collection trays 36, whereby fluid communicationbetween the tube sheets or collection trays 36 is achieved. Lateralmovement of slider valve 42 positions valve 42 such that fluidcommunication between the adjacent tube sheets or collection tubes 36 isinterrupted. Change in the position of slider valve 42 can be achievedby such means as magnetic force that may be remotely activated.

[0036] In a further embodiment, depicted in FIG. 4, “tell discs” 46 areprovided. Tell disc 46 is buoyant and provides a means to indicate thefluid level within tube 44. In another embodiment, tell disc 46 iscapable of sealing the bottom of tube 44 in the absence of fluid.

[0037]FIG. 5 depicts a further embodiment of the invention, apparatus48. Attached to electronic receiver 50, which can be magneticallyactivated and remotely controlled, are rotor arms 16 connected via hinge28 to a series of stacked trays 52. The application of a centrifugalforce will raise stacked trays 52 to be parallel with the centrifugalforce. In a series of steps, magnetic couplers 54 can be sequentiallyactivated and deactivated to manipulate valves within stacked trays 52,thereby selectively directing flow of proteome washes and eluentsthrough affinity arrays 34 of stack trays 52. In a detailed schematicshown in FIG. 6, selective direction of flow through the individualtrays in stack 52 is depicted. The flow of each solution through anarray is indicated as magnetic coupler 54 activates and deactivates theopening and closing of the connecting orifices between trays of stack52.

[0038] The eluate obtained using the method and apparatus of theinvention is subsequently characterized by SDS-PAGE, MALDI-TOF massspectrometry, liquid chromatography electrospray ionization tandem massspectrometry (LC ESI MS/MS) or ICAT mass spectrometry, or by othersuitable methods as will be appreciated by one of skill in the art, toidentify fractions that contain either single proteins, or a mixture ofa small number of proteins. These fractions are further analyzed bymicrosequencing. Mixed peptide sequencing may be performed as describedin Damer et al., (1998) J. Biol. Chem. 273: 24396-24405; Alms et al.,(1999) EMBO J. 18: 4157-4168, the teachings of which are incorporatedherein by reference in their entirety. The mixed sequence data issubsequently processed using the algorithms, for example, FASTF orTFASTF, to sort and match the data with protein and DNA databases,respectively. Alternatively, other algorithms can be utilized to analyzethe sequence data as will be appreciated by those who are skilled in theart. The biological significance of the identified protein is thenassessed.

[0039] One embodiment of an apparatus for identifying eluate proteins isdepicted in FIG. 7. As shown in FIG. 7, apparatus 56 includes affinityarray 34 which interfaces with collection tray 36, also referred toherein as capture array 36, such that elution of eluates bycentrifugation captures the eluates in collection tray 36. In apreferred embodiment, column 37 of collection tray 36 containshydrophobic resin 58. Hydrophobic resins suitable for use in theinvention will be recognized by those of skill in the art. Withoutlimitation, an example of a suitable hydrophobic resin include POROS®R2. In one embodiment, the amount of hydrophobic resin 58 is betweenabout 2 μl and about 4 μl. Subsequently, collection array 36 isdisengaged from affinity array 34 and the eluate contained in collectionarray 36 is washed using buffers suitable for removal of unboundcomponents and/or drug molecule(s), as will be appreciated by one ofskill in the art. Collection array 36 is then washed with buffer, suchas a protease buffer, and incubated with, for example, buffer containinga digestive enzyme, such as trypsin. Fluid flow through collection array36 is stopped, preferably for a period of time in a range of betweenabout 6 hours and about 8 hours, before collection array 36 isinterfaced with nano-needle array 60 and centrifuged to collect digestedeluate in nano-needle array 60. Other methods to digest or otherwisefractionate the eluate into a preparation suitable for analysis, forexample, by mass spectrometry, will be appreciated by one of ordinaryskill in the art. Digested eluate from column 37 of collection array 36elutes into a corresponding nano-needle 62 of nano-needle array 60.

[0040] Following collection of digested eluate in nano-needle array 60,nano-needle array 60 is disengaged from collection array 36 and placedinto manifold 66, as depicted in apparatus 64 of FIG. 8. Manifold 66positions nano-needle array 60 in front of mass spectrometer orifice 68.In a preferred embodiment, the mass spectrometer is suitable forelectrospray ionization (ESI). In an alternative embodiment, the massspectrometer is suitable for matrix assisted laser desorbtion ionization(MALDI) mass spectrometry. Precise alignment of each nano-needle 62 withmass spectrometer orifice 68 can be achieved by two-dimensional movementof manifold 66. Hollow push rod 70 engages at the back of nano-needle62, and mechanically pushes the needle tip of nano-needle 62 to massspectrometer orifice 68. Application of air pressure by means ofdirecting air flow through flexible pipe 72 causes the spraying ofdigested eluate from nano-needle 62 into mass spectrometer orifice 68,thereby mediating mass spectrometry fingerprint analysis of digestedeluate. After mass spectrometry analysis, push rod 70 is retracted andengaged with the next aligned nano-needle 62. In a preferred embodiment,coordinated movement of push rod 70 and mass spectrometer dataacquisition is computer-controlled. A detailed schematic of nano-needle62 alignment with mass spectrometer orifice 68 and engagement of pushrod 70 is provided in FIG. 9.

EQUIVALENTS

[0041] While this invention has been particularly shown and describedwith references to preferred embodiments thereof, it will be understoodby those skilled in the art that various changes in form and details maybe made therein without departing from the scope of the inventionencompassed by the appended claims.

What is claimed is:
 1. A method for screening a proteome, comprising thesteps of: a) directing compounds of a proteome through an array ofaffinity elements, whereby at least one compound of the proteome bindsspecifically to at least one of said affinity elements; b) washing thearray, whereby non-specifically bound compounds of the proteome areeluted from the array; and c) directing at least one eluent through thearray by centrifugal force, wherein said eluent releases said boundcompound, whereby said compound is eluted from the affinity element as acomponent of an eluate, thereby screening the proteome.
 2. The method ofclaim 1, wherein at least one element of the array of affinity elementsincludes at least one physiologic target candidate of a proteincomponent of the proteome.
 3. The method of claim 2, wherein thephysiologic target candidate is adenosine triphosphate or a structuralanalog thereof.
 4. The method of claim 3, wherein the target candidateis adenosine triphosphate.
 5. The method of claim 4, wherein theadenosine triphosphate is bound to an inert support of the element in auniform orientation.
 6. The method of claim 5, wherein the adenosinetriphosphate is bound to the inert support at a gamma phosphate portionof the adenosine triphosphate, whereby an adenosine portion of theadenosine triphosphate is exposed to solutions directed through thearray.
 7. The method of claim 6, wherein the eluent includes purine orat least one purine analog.
 8. The method of claim 7, wherein the purineanalog is a naturally-occurring purine analog.
 9. The method of claim 8,wherein the purine analog is selected from the group consisting of NADH,AMP, ADP and ATP.
 10. The method of claim 5, wherein the concentrationof adenosine triphosphate on at least a portion of the elements is in arange of between about 10 and about 50 μmoles per milliliter of theelement.
 11. The method of claim 10, wherein the concentration ofadenosine triphosphate is about 10 μmoles per milliliter of the element.12. The method of claim 5, wherein the amount of proteome directedthrough the array is sufficient to recover between about 0.1 pmol andabout 1 pmol of a component of the proteome that binds to adenosinetriphosphate.
 13. The method of claim 12, wherein the eluent has aconcentration of protein in a range of between about 0.1 mg/ml and about1 g/ml.
 14. The method of claim 13, wherein the concentration of proteinin the eluent is about 10 mM.
 15. The method of claim 1, whereincompounds of the proteome are directed through the affinity elements bycentrifugal force.
 16. The method of claim 15, wherein the array iswashed by directing a wash solution through the array by centrifugalforce.
 17. The method of claim 1, wherein each array includes at leasttwelve elements.
 18. The method of claim 1, wherein each array includesat least ninety-six elements.
 19. The method of claim 1, wherein atleast a portion of the elements of the array includes an amount of resinpacking in a range of between about 50 μl and about 100 μl.
 20. Themethod of claim 19, wherein the amount of eluent directed through eacharray element is in a range of between about 10 μl and about 100 μl. 21.The method of claim 1, wherein the eluate is analyzed to identify elutedcomponents of the proteome.
 22. The method of claim 1, wherein theeluent includes at least a portion of a chemical library.
 23. The methodof claim 1, wherein each element of the affinity array includes at leasta portion of a chemical library.
 24. The method of claim 1, wherein theelements of the affinity array and the eluent each includes a portion ofat least one chemical library.
 25. The method of claim 1, wherein theproteome is distributed among elements of the affinity array.
 26. Themethod of claim 1, wherein the proteome is screened for components thatare eluted from an element of the affinity array by competitive bindingwith an eluent comprising a proteome component.
 27. The method of claim1, wherein the proteome is screened for components that are eluted froman element of the affinity array by competitive binding with an eluentcomprising an element of the affinity array.
 28. The method of claim 1,wherein the proteome is screened for components that are eluted from anelement of the affinity array by competitive binding with an eluentcomprising a chemical library component.
 29. The method of claim 1,wherein each array element includes a plurality of ligands.
 30. Themethod of claim 29, wherein each array element includes at least tenligands.
 31. The method of claim 1, wherein each eluent that is directedthrough an array element includes a plurality of distinct proteincomponents that are candidates for selective release and elution of aproteome component from an affinity element.
 32. The method of claim 31,wherein each eluent component includes at least ten distinct proteincomponents that are candidates for selective release of a proteomecomponent from an affinity element.
 33. The method of claim 1, whereinthe elements of the affinity array include a ligand that is bound to aninert support of each element in an orientation that is distinct fromthe orientation of the same ligand in at least one other element. 34.The method of claim 1, further including analyzing the eluate by thesteps: a) first treating the eluate with an agent to fractionate theeluate; and b) analyzing the fractionated eluate by nano-spray massspectrometry, thereby analyzing the eluate.
 35. The method of claim 34,wherein the nano-spray mass spectrometry is electrospray ionization. 36.The method of claim 35, wherein the electro spray ionization massspectrometry is performed using a nano-needle array.
 37. The method ofclaim 34, wherein the agent to fractionate the eluate is an enzyme. 38.The method of claim 37, wherein the enzyme is trypsin.
 39. An apparatusfor screening a proteome, comprising: a) an array of affinity elements,said affinity elements including at least one ligand; and b) means forapplying centrifugal force to said array, whereby an eluent can bedirected through the array by centrifugal force and can release acompound of the proteome that is bound to the ligand, thereby elutingthe compound from the affinity element as a component of an eluate andscreening the proteome.
 40. The apparatus of claim 39, wherein the meansfor applying centrifugal force includes a swing basket supporting thearray, said swing basket including a hinge, whereby rotation of theswing basket about an axis causes the swing basket to rotate about thehinge, thereby causing centrifugal force on the affinity array to beparallel to an overall path of flow of eluent through elements of saidarray.
 41. The apparatus of claim 40, further including at least onetube sheet, whereby tube elements of the tube sheet can align withelements of the affinity array.
 42. The apparatus of claim 41, whereinthe tube sheet is positioned between the hinge and the affinity array.43. The apparatus of claim 42, further including collection tubes thatcan be aligned with the elements of the affinity array, said collectiontubes being positioned on a side of the affinity array opposite to thatof the tube sheet.
 44. The apparatus of claim 43, wherein the tube sheetis moveable laterally relative to the flow of liquid from the tube sheetthrough the affinity array.
 45. The apparatus of claim 44, wherein thetube sheet further defines orifices between at least a portion of tubesof the tube sheet.
 46. The apparatus of claim 45, wherein the tube sheetis moveable between at least three positions, wherein each element ofthe affinity array is aligned with two different tubes of the tube sheetin two of the position, and aligned with an orifice in the thirdposition.
 47. The apparatus of claim 46, further including a centrifugebasket within which the swing basket is supported.
 48. The apparatus ofclaim 47, further including means for continuous directing at least onewash solution through the affinity array.
 49. The apparatus of claim 48,further including a wash solution source, and wherein the affinity arrayis in fluid communication with the wash solution source when theorifices of the tube sheet are aligned with elements of the affinityarray.
 50. The apparatus of claim 41, wherein the tube sheet includestubes that contain at least a portion of a proteome.
 51. The apparatusof claim 50, wherein elements of the tube sheet include distinctcomponents or combinations of components of the proteome.
 52. Theapparatus of claim 51, wherein elements of the tube sheet containcomponents of a chemical library.
 53. The apparatus of claim 52, whereinelements of the tube sheet include distinct components or combinationsof components of the chemical library.
 54. The apparatus of claim 53,wherein movement of the tube sheet relative to the affinity array causeselements of the array to be aligned and in fluid communication witheither elements of the tube sheet containing components of a proteome,orifices of the tube sheet whereby fluid communication is establishedwith a wash source, or elements of the tube sheet containing componentsof a chemical library.
 55. The apparatus of claim 54, further includingmagnetic means for moving the tube sheet.
 56. The apparatus of claim 55,wherein the collection tubes are moveable between a position that causeseluate from the affinity array to be collected in the centrifuge basketand a position that causes eluate from the affinity array to becollected in the collection tubes.
 57. The apparatus of claim 56,wherein the collection tubes are aligned for collection of eluate whenthe tube sheet is aligned for delivery of components of a chemicallibrary to the affinity array.
 58. The apparatus of claim 57, whereinthe elements of the tube sheet each include a disc that indicates thelevel of fluid in each element.
 59. The apparatus of claim 41, includinga plurality of tube sheets at least one tube sheet containing at least aportion of a proteome, and at least one tube sheet containing componentsof a chemical library.
 60. The apparatus of claim 59, wherein the tubesheets are stacked.
 61. The apparatus of claim 60, further includingmeans for selectively directing proteome wash or combinatorial librarycomponents through elements of the affinity array.
 62. The apparatus ofclaim 39 further including a nano-needle array, wherein the nano-needlearray is aligned with the array of affinity elements, such that thenano-needle array collects the eluate.
 63. The apparatus of claim 62,wherein a nano-needle of the nano-needle array further includes anamount of hydrophobic resin in a range of between about 2 μl and about 4μl.
 64. The apparatus of claim 63, wherein the nano-needle array can bedetached from the array of affinity elements and mounted in a massspectrometer, such that a nano-needle of the nano-needle array isaligned with an inlet orifice of the mass spectrometer for delivery ofeluate to be analyzed by mass spectrometry.
 65. The apparatus of claim64, wherein the mass spectrometry is nano-spray mass spectrometry. 66.The apparatus of claim 65, wherein the nano-spray mass spectrometry iselectrospray ionization.
 67. The apparatus of claim 66, wherein thedelivery of the eluate to be analyzed by mass spectrometry is mediatedby air pressure directed through a hollow push rod that is attached tothe nano-needle that contains the eluate, thereby producing a spray ofeluate directed into the inlet orifice of the mass spectrometer, thusdelivering the eluate into the mass spectrometer for analysis.
 68. Theapparatus of claim 67, wherein the nano-needle array can be moved in atleast two dimensions to align a nano-needle of the nano-needle arraywith the inlet orifice of the mass spectrometer for delivery of theeluate to be analyzed by mass spectrometry.
 69. The apparatus of claim68, wherein the alignment of a nano-needle of the nano-needle array iscontrolled by a computer.